MIC-Tandem: Parallel X!Tandem Using MIC on Tandem Mass Spectrometry Based Proteomics Data

Pinjie He, Kenli Li
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引用次数: 3

Abstract

The widespread use of mass spectrometry for protein identification has created an urgent demand for improving computational efficiency of matching mass spectrometry data to protein databases. With the rapid development of chip technology and parallel computing technique, such as multi-core processor, many-core coprocessor and cluster of multi-node, the speed and performance of the major mass spectral search engines are continuously improving. In recent ten years, X!Tandem as a popular and representative open-source program in searching mass spectral has extended several parallel versions and obtains considerable speedups. However, because these parallel strategies are mainly based on cluster of nodes, higher costs (e.g., charge of electricity and maintenance) is needed to get limited speedups. Fortunately, Intel Many Integrated Core (MIC) architecture and Graphics Processing Unit (GPU) are ideal for this problem. In this paper, we present and implement a parallel strategy to X!Tandem using MIC called MIC-Tandem, That shows excellent speedups on commodity hardware and produces the same results as the original program.
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MIC-Tandem:平行X!基于串联质谱的蛋白质组学数据串联使用MIC
质谱法在蛋白质鉴定中的广泛应用,迫切需要提高质谱数据与蛋白质数据库匹配的计算效率。随着多核处理器、多核协处理器、多节点集群等芯片技术和并行计算技术的快速发展,各大质谱搜索引擎的速度和性能都在不断提高。近十年来,X!Tandem作为一个流行且具有代表性的质谱搜索开源程序,扩展了多个并行版本,并获得了相当大的速度提升。然而,由于这些并行策略主要基于节点集群,因此需要更高的成本(例如,电费和维护费用)来获得有限的速度。幸运的是,英特尔多集成核心(MIC)架构和图形处理单元(GPU)是解决这个问题的理想选择。在本文中,我们提出并实现了X!使用称为MIC-Tandem的MIC串联,它在商用硬件上显示出出色的加速,并产生与原始程序相同的结果。
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